How to generate Links in WWW BLAST server ??

[David Coornaert]

hmm it seems to me that
using ncbi's version,
u'll have links in the output, ONLY if your databank entries
have valids "gi" in their definition line
make urself a very small databank of a few seq
each of the kind :

 >gi 0001|whatevergene001|unfortunatilis microbus gene xyz
atcgtgtca...
 >gi 0002|
etc etc

formatdb this, and you're ok ! (if it's ok, formatdb will generate two 
extra files as compared to banks without "gi")
of course the links that any-blast-prgm will generate, will all point 
toward NCBI's fetchentry script, hence, you'll still have to substitute 
the output with one-of-yours script able to "fastacmd" the appropriate 
gi from the appropriate db..since the gi you supplied are strictly yours.


Hope it helps,
David Coornaert




Simon Andrews wrote:

> Ingo Klein wrote:
> 
>>Hi yall,
>>I'm setting up a WWW BLAST server for a friend.
>>The Searchengine is up and running happy.
>>
>>The only problem is :
>>
>>If I search a sequence in the NCBI-Test database, I get links for
>>further information about the found sequence. If I do the same with
>>our generated database, these links are missing...
>>
>>Any Help,Links,Sources or what ever whould be nice...
>>
> 
> 
> Funny you should ask - I'm just doing this myself!  In our case I have a
> subroutine in the blast CGI script which monitors the blast output
> stream and looks for a particular pattern (whatever describes the
> sequence identifiers in your database).  Where it finds a sequence name,
> it substitutes it for a link containing the same text, with a hyperlink
> to another CGI script to get more info.
> 
> In our case, the link is to another internal script, but you could link
> out to NCBI or whatever you want.
> 
> I don't know what language you're using to write your CGI in, but in
> Perl the relevant bit of our script looks like (this isn't exact and is
> untested, but should give you an idea);
> 
> while (<PIPEOUTOFBLAST>) {
> 
> 	if (/Pattern_for_seq_name/){
> 
> 		s#(Pattern_for_seq_name)#<a href="http://whaterer.link?id=$1>$1</a>#;
> 	}	
> 
> 	print;
> }
> 
> This assumes that you are running blastall with the -T option, so you
> are generating HTML anyway.
> 
> Hope this helps
> 
> Simon.
> 
>